PhD Chapter 1
Campaign 2014 - Maps and exploration
This series of files compile analyses done for the specific analysis of Chapter 1, for the local campaign of 2014.
All analyses have been done with PRIMER-e 6 and R 4.0.2.
Click on the table of contents in the left margin to assess a specific analysis.
Click on a figure to zoom it
We used data from subtidal ecosystems (see metadata files for more information). Only stations that have been sampled both for abiotic parameters and benthic species were included.
Selected variables for the analyses:
- Percentage of organic matter: om
- Percentage of gravel: gravel
- Percentage of sand: sand
- Percentage of silt: silt
- Percentage of clay: clay
- Concentration of arsenic: arsenic
- Concentration of cadmium: cadmium
- Concentration of chromium: chromium
- Concentration of copper: copper
- Concentration of iron: iron
- Concentration of manganese: manganese
- Concentration of mercury: mercury
- Concentration of lead: lead
- Concentration of zinc: zinc
- Specific richness: S
- Total density of individuals: N
- Shannon’s diversity: H
- Piélou’s evenness: J
Abundances of Bipalponephtys neotena (Bneo) and Spisula solidissima (Ssol) were also considered (see IndVal and SIMPER results).
Statistics for each variable considered:
| Mean | SD | SE | Median | Min | Max | 95% CI | |
|---|---|---|---|---|---|---|---|
| om | 2.265 | 1.630 | 0.364 | 2.016 | 0.278 | 8.260 | 0.714 |
| gravel | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| sand | 0.050 | 0.224 | 0.050 | 0.000 | 0.000 | 1.000 | 0.098 |
| silt | 0.001 | 0.000 | 0.000 | 0.001 | 0.000 | 0.001 | 0.000 |
| clay | 0.949 | 0.223 | 0.050 | 0.999 | 0.000 | 1.000 | 0.098 |
| arsenic | 3.345 | 1.424 | 0.319 | 3.150 | 1.100 | 6.000 | 0.624 |
| cadmium | 0.131 | 0.040 | 0.009 | 0.135 | 0.040 | 0.190 | 0.018 |
| chromium | 72.875 | 25.652 | 5.736 | 75.850 | 31.700 | 143.300 | 11.242 |
| copper | 17.640 | 6.952 | 1.555 | 18.850 | 3.300 | 32.400 | 3.047 |
| iron | 69456.658 | 31948.948 | 7144.002 | 64356.210 | 32899.910 | 188857.220 | 14001.986 |
| manganese | 1934.067 | 1243.717 | 278.104 | 1475.005 | 705.690 | 5962.190 | 545.073 |
| mercury | 0.029 | 0.058 | 0.013 | 0.015 | 0.000 | 0.250 | 0.025 |
| lead | 6.278 | 2.988 | 0.668 | 6.240 | 1.020 | 12.180 | 1.310 |
| zinc | 70.030 | 22.198 | 4.964 | 71.550 | 15.900 | 101.500 | 9.728 |
| S | 25.250 | 6.463 | 1.445 | 27.000 | 10.000 | 34.000 | 2.833 |
| N | 1140.150 | 665.407 | 148.790 | 1322.500 | 36.000 | 2103.000 | 291.622 |
| H | 1.866 | 0.338 | 0.075 | 1.882 | 1.246 | 2.737 | 0.148 |
| J | 0.590 | 0.121 | 0.027 | 0.585 | 0.409 | 0.929 | 0.053 |
| Mean | SD | SE | Median | Min | Max | 95% CI | |
|---|---|---|---|---|---|---|---|
| om | 0.471 | 0.238 | 0.053 | 0.385 | 0.187 | 0.877 | 0.104 |
| gravel | 0.034 | 0.106 | 0.024 | 0.007 | 0.000 | 0.481 | 0.046 |
| sand | 0.247 | 0.439 | 0.098 | 0.000 | 0.000 | 1.000 | 0.192 |
| silt | 0.008 | 0.007 | 0.001 | 0.008 | 0.000 | 0.022 | 0.003 |
| clay | 0.711 | 0.433 | 0.097 | 0.968 | 0.000 | 0.993 | 0.190 |
| arsenic | 2.095 | 0.633 | 0.142 | 1.950 | 1.400 | 3.700 | 0.277 |
| cadmium | 0.101 | 0.045 | 0.010 | 0.090 | 0.030 | 0.220 | 0.020 |
| chromium | 58.165 | 32.082 | 7.174 | 53.400 | 10.900 | 125.000 | 14.060 |
| copper | 4.450 | 3.818 | 0.854 | 3.250 | 2.200 | 19.400 | 1.673 |
| iron | 58989.194 | 31326.220 | 7004.756 | 55172.005 | 14089.920 | 146603.720 | 13729.069 |
| manganese | 890.020 | 383.078 | 85.659 | 927.960 | 251.670 | 1638.110 | 167.888 |
| mercury | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| lead | 2.337 | 0.836 | 0.187 | 2.225 | 1.090 | 4.960 | 0.367 |
| zinc | 36.295 | 8.823 | 1.973 | 36.150 | 18.400 | 55.300 | 3.867 |
| S | 15.700 | 6.208 | 1.388 | 16.000 | 6.000 | 35.000 | 2.721 |
| N | 141.800 | 219.010 | 48.972 | 64.000 | 14.000 | 941.000 | 95.984 |
| H | 1.813 | 0.479 | 0.107 | 1.953 | 0.911 | 2.457 | 0.210 |
| J | 0.681 | 0.175 | 0.039 | 0.678 | 0.315 | 0.938 | 0.077 |
1. Maps
1.1. General map
1.2. Parameters maps
For maps of heavy metal concentrations, stations have been grouped based on Environment Canada (2007) classification of sediment toxicity (grey = low toxicity, red = high toxicity).
OM
Gravel
Sand
Silt
Clay
Arsenic
Cadmium
Chromium
Copper
Iron
Manganese
Mercury
Lead
Zinc
Species
Richness
Density
Diversity
Evenness
2. Figures
2.1. Barplots
Organic matter
Grain-size
Heavy metals
Species abundances
Diversity indices
2.2. Phylum frequencies
Conditions
| Phylum | HI | R |
|---|---|---|
| Annelida | 20360 | 1135 |
| Phoronida | 1138 | 2 |
| Arthropoda | 883 | 749 |
| Mollusca | 361 | 743 |
| Cnidaria | 42 | 40 |
| Bryozoa | 8 | 22 |
| Platyhelminthes | 5 | 0 |
| Echinodermata | 4 | 139 |
| Hemichordata | 2 | 0 |
| Chaetognatha | 0 | 1 |
| Nematoda | 0 | 0 |
| Nemertea | 0 | 5 |
| Sipuncula | 0 | 0 |
Sites
| Phylum | P1 | P2 | P3 | P4 | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|---|---|
| Annelida | 6065 | 7459 | 6155 | 681 | 43 | 106 | 926 | 60 |
| Phoronida | 408 | 317 | 412 | 1 | 0 | 0 | 1 | 1 |
| Arthropoda | 289 | 317 | 219 | 58 | 40 | 281 | 399 | 29 |
| Mollusca | 60 | 113 | 80 | 108 | 30 | 381 | 110 | 222 |
| Cnidaria | 13 | 11 | 9 | 9 | 11 | 15 | 7 | 7 |
| Bryozoa | 4 | 1 | 0 | 3 | 0 | 14 | 2 | 6 |
| Echinodermata | 4 | 0 | 0 | 0 | 20 | 65 | 49 | 5 |
| Platyhelminthes | 1 | 0 | 4 | 0 | 0 | 0 | 0 | 0 |
| Chaetognatha | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 |
| Hemichordata | 0 | 0 | 2 | 0 | 0 | 0 | 0 | 0 |
| Nematoda | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Nemertea | 0 | 0 | 0 | 0 | 0 | 5 | 0 | 0 |
| Sipuncula | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
2.3. Species estimation curves
2.4. Principal Component Analysis
Parameters + Metals
Variables have been standardized by mean and standard-deviation.
Parameters
Variables have been standardized by mean and standard-deviation.
Metals
Variables have been standardized by mean and standard-deviation.
2.5. Non-metric Multidimensional Scaling
Parameters + Metals
Variables have been standardized by mean and standard-deviation.
Parameters
Variables have been standardized by mean and standard-deviation.
Metals
Variables have been standardized by mean and standard-deviation.
Species
Stations with no species were deleted from this analysis.
2.6. Hierarchical Agglomerative Clustering
Parameters + Metals
Variables have been standardized by mean and standard-deviation.
## 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30
## 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 3 1 3 3 3 3 3 2 3 3 3 2
## 31 32 33 34 35 36 37 38 39 40
## 2 3 2 3 2 3 3 3 3 3
Parameters
Variables have been standardized by mean and standard-deviation.
## 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30
## 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 3 3 3 3 3 2 3 3 3 2
## 31 32 33 34 35 36 37 38 39 40
## 2 3 2 3 2 3 3 3 3 3
Metals
Variables have been standardized by mean and standard-deviation.
## 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30
## 1 2 1 1 1 1 2 1 1 1 2 3 2 2 2 3 3 2 2 2 2 2 2 3 2 3 3 3 3 3
## 31 32 33 34 35 36 37 38 39 40
## 3 3 3 3 3 2 2 3 3 3
Species
Stations with no species were deleted from this analysis.
## 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30
## 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 1 2 2 2 2 2 2 2 2 2 2
## 31 32 33 34 35 36 37 38 39 40
## 2 2 2 2 2 2 2 2 2 2